B-cell epitopes are the sites of molecules that are recognized by antibodies of the immune system. Identification of B-cell epitopes in therapeutic proteins can be useful in designing variants that do not elicit an immune response when adminstered to patients.
B-cell epitopes can be identified by individually mutating amino acids of a protein, typically with alanine (alanine scanning), and determining the effect of each mutation on antibody binding (Onda et al., 2011, Proc. Natl. Acad. Sci. 108(14):5742-7). A disruption of protein-antibody binding following mutagenesis indicates that the mutated residue is part of a B-cell epitope recognized by the antibody. It has been found that even a single mutation in a B-cell epitope can eliminate binding to a panel of antibodies directed to the protein, and that immunogenicity of a protein can be reduced by the introduction of mutations in a B-cell epitope (Nagata and Pastan, 2009, Advanced Drug Delivery Reviews 61:977-985). However, this approach is also time consuming and labor intensive. Moreover, alanine scanning does not necessarily identify mutations that would provide the greatest reduction in immunogenicity.
Thus, there is a need for a simple, non-labor intensive yet comprehensive method which allows for the identification and elimination of B-cell epitopes.